The taxonomic identity of canids of the genus Canis in North Africa has been investigated using molecular phylogenetic analysis based on Cytochrome b mitochondrial DNA sequence analysis. Tissue samples from 18 Canis specimens collected from all known populations/taxa in Egypt were obtained and analyzed. The resulting Cyt b mt DNA sequences of current Canis taxa, described based morphological characters were compared to each other and to other Canis populations/taxa across North Africa and the Middle East. The results showed no detectable sequence differentiation among all populations, suggesting that the separation of the phenotypically differentiated populations of Egypt has been relatively recent. Estimate divergence time between different phylogroups of the genus and the phylogeographic history of the genus was discussed in a regional paleogeographic context.